Running Clock Question

[SCalScoreKeeper]

Had this exact debate with an official in our area at a GV december tourney my school hosts-

A is up by 39 points and is fouled while driving to the basket! A5 shoots the first free throw and makes it putting us into the "window".B calls timeout.Official in question instructs us to run the clock coming out of timeout. We run it knowing that doing so is incorrect by rule and an official coming in for the next slate of games tells us she was wrong.

I believe that the clock should start either on a make or rebound from the missed attempt.

Question for those who work in Mississippi-

Why would you stop clock for free throws in the final two minutes? Here is our rule-

1607. MERCY RULE
When at the conclusion of the third quarter, or any point thereafter, if there is a point differential of 40 or more points,a running clock shall be instituted for the remainder of the game, regardless of the score. This applies to all levels of play. (ApprovedMay 2004 Federated Council)

The only time that a running clock can be stopped is for an timeout on the floor!